Starting phenix.real_space_refine on Sun Aug 24 18:33:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tjn_41305/08_2025/8tjn_41305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tjn_41305/08_2025/8tjn_41305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tjn_41305/08_2025/8tjn_41305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tjn_41305/08_2025/8tjn_41305.map" model { file = "/net/cci-nas-00/data/ceres_data/8tjn_41305/08_2025/8tjn_41305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tjn_41305/08_2025/8tjn_41305.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 77 5.16 5 C 13698 2.51 5 N 3910 2.21 5 O 4217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21903 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 883, 6556 Classifications: {'peptide': 883} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 830} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1, '4HH:plan-3': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 9300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1257, 9300 Classifications: {'peptide': 1257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 68, 'TRANS': 1188} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1450 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1565 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1493 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 181} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.28, per 1000 atoms: 0.20 Number of scatterers: 21903 At special positions: 0 Unit cell: (112.2, 176, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 1 15.00 O 4217 8.00 N 3910 7.00 C 13698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 799.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5300 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 29 sheets defined 33.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 7 through 33 removed outlier: 3.550A pdb=" N GLU B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 120 through 138 removed outlier: 4.105A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.671A pdb=" N LEU B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.945A pdb=" N GLY B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 312 through 327 removed outlier: 3.913A pdb=" N GLN B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.272A pdb=" N ILE B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.826A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 4.057A pdb=" N ARG B 363 " --> pdb=" O GLY B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.546A pdb=" N LEU B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 530 through 542 Processing helix chain 'B' and resid 570 through 574 removed outlier: 3.507A pdb=" N ALA B 573 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL B 574 " --> pdb=" O GLY B 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 570 through 574' Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 587 through 599 Proline residue: B 596 - end of helix Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 624 through 645 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 657 through 667 removed outlier: 4.477A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 679 removed outlier: 4.025A pdb=" N ARG B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 824 Processing helix chain 'B' and resid 837 through 848 removed outlier: 3.802A pdb=" N ILE B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 removed outlier: 3.919A pdb=" N PHE B 868 " --> pdb=" O SER B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.738A pdb=" N VAL B 887 " --> pdb=" O ASP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1428 Processing helix chain 'B' and resid 1448 through 1464 removed outlier: 3.550A pdb=" N GLU B1454 " --> pdb=" O LEU B1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1475 Processing helix chain 'B' and resid 1477 through 1487 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.685A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 removed outlier: 3.567A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.890A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.518A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 312 through 328 removed outlier: 4.342A pdb=" N GLN A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.990A pdb=" N ILE A 334 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.758A pdb=" N ILE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.785A pdb=" N SER A 374 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.562A pdb=" N THR A 513 " --> pdb=" O TYR A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.660A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 580 through 595 removed outlier: 3.517A pdb=" N CYS A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 removed outlier: 3.939A pdb=" N PHE A 605 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 645 Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 670 through 683 Processing helix chain 'A' and resid 812 through 824 Processing helix chain 'A' and resid 836 through 847 removed outlier: 4.278A pdb=" N ALA A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.792A pdb=" N THR A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.596A pdb=" N ALA A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1078 Processing helix chain 'A' and resid 1093 through 1100 removed outlier: 3.884A pdb=" N HIS A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1151 through 1164 Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1182 through 1192 Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1240 through 1248 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.916A pdb=" N VAL A1252 " --> pdb=" O SER A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1305 removed outlier: 4.134A pdb=" N GLY A1291 " --> pdb=" O GLY A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1340 through 1354 removed outlier: 3.565A pdb=" N ALA A1344 " --> pdb=" O PRO A1340 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A1345 " --> pdb=" O PRO A1341 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1374 Processing helix chain 'A' and resid 1385 through 1390 removed outlier: 4.258A pdb=" N ARG A1390 " --> pdb=" O ASP A1387 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.540A pdb=" N SER D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.029A pdb=" N LEU B 367 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 370 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 336 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 296 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 455 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU B 294 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 276 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N MET B 40 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET B 274 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N CYS B 42 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA B 272 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 200 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 200 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 151 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 201 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 153 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 227 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 231 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 272 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N CYS A 42 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 274 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET A 40 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 276 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 294 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU A 455 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 296 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 336 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 370 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU A 367 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA3, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AA5, first strand: chain 'B' and resid 649 through 654 removed outlier: 6.403A pdb=" N ALA B 558 " --> pdb=" O PRO B 649 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 651 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 653 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 559 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 784 through 786 removed outlier: 4.233A pdb=" N PHE B 784 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.604A pdb=" N GLU A 427 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 561 removed outlier: 6.373A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 828 " --> pdb=" O ILE A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1120 through 1127 removed outlier: 4.289A pdb=" N VAL A1120 " --> pdb=" O THR A 937 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 935 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA A1313 " --> pdb=" O VAL A1361 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER A1274 " --> pdb=" O TRP A1314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 974 through 977 removed outlier: 6.494A pdb=" N GLY A 947 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 977 " --> pdb=" O GLY A 947 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP A 949 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR A 948 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A1002 " --> pdb=" O THR A 948 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1169 through 1170 removed outlier: 6.934A pdb=" N THR A1142 " --> pdb=" O ALA A1223 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE A1225 " --> pdb=" O THR A1142 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A1144 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A1222 " --> pdb=" O ALA A1269 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL A1271 " --> pdb=" O SER A1222 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL A1224 " --> pdb=" O VAL A1271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 25 Processing sheet with id=AB5, first strand: chain 'C' and resid 62 through 63 removed outlier: 5.235A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 36 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 96 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.716A pdb=" N THR C 158 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.694A pdb=" N ASP D 127 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 57 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR D 70 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP D 56 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 70 " --> pdb=" O ASN D 74 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN D 74 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB9, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AC1, first strand: chain 'D' and resid 167 through 170 removed outlier: 4.001A pdb=" N LYS D 167 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 219 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 218 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 227 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AC3, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.793A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE E 52 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET E 36 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 149 through 152 removed outlier: 6.255A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 184 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL E 176 " --> pdb=" O SER E 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AC7, first strand: chain 'F' and resid 28 through 29 Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AC9, first strand: chain 'F' and resid 66 through 69 removed outlier: 5.535A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F 69 " --> pdb=" O TRP F 56 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 138 through 140 removed outlier: 3.748A pdb=" N LEU F 157 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE F 140 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 155 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN F 182 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 167 through 168 removed outlier: 3.563A pdb=" N LYS F 167 " --> pdb=" O THR F 219 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 219 " --> pdb=" O LYS F 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 809 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7501 1.34 - 1.46: 4963 1.46 - 1.58: 9766 1.58 - 1.70: 2 1.70 - 1.82: 120 Bond restraints: 22352 Sorted by residual: bond pdb=" N VAL B 684 " pdb=" CA VAL B 684 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.35e+00 bond pdb=" N ILE B 685 " pdb=" CA ILE B 685 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N LEU B 837 " pdb=" CA LEU B 837 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.52e-02 4.33e+03 3.82e+00 bond pdb=" CA VAL D 154 " pdb=" CB VAL D 154 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.60e+00 bond pdb=" CA VAL B 684 " pdb=" C VAL B 684 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.27e-02 6.20e+03 1.59e+00 ... (remaining 22347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 30034 2.37 - 4.74: 322 4.74 - 7.10: 34 7.10 - 9.47: 13 9.47 - 11.84: 4 Bond angle restraints: 30407 Sorted by residual: angle pdb=" CA LYS B1414 " pdb=" CB LYS B1414 " pdb=" CG LYS B1414 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" C PRO C 154 " pdb=" N GLU C 155 " pdb=" CA GLU C 155 " ideal model delta sigma weight residual 121.80 132.60 -10.80 2.44e+00 1.68e-01 1.96e+01 angle pdb=" CB MET A1339 " pdb=" CG MET A1339 " pdb=" SD MET A1339 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CA MET A1339 " pdb=" CB MET A1339 " pdb=" CG MET A1339 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA GLU F 102 " pdb=" CB GLU F 102 " pdb=" CG GLU F 102 " ideal model delta sigma weight residual 114.10 121.57 -7.47 2.00e+00 2.50e-01 1.40e+01 ... (remaining 30402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11691 17.81 - 35.62: 1239 35.62 - 53.43: 309 53.43 - 71.24: 58 71.24 - 89.05: 32 Dihedral angle restraints: 13329 sinusoidal: 5051 harmonic: 8278 Sorted by residual: dihedral pdb=" CB CYS F 39 " pdb=" SG CYS F 39 " pdb=" SG CYS F 109 " pdb=" CB CYS F 109 " ideal model delta sinusoidal sigma weight residual -86.00 -161.91 75.91 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS D 156 " pdb=" SG CYS D 156 " pdb=" SG CYS D 216 " pdb=" CB CYS D 216 " ideal model delta sinusoidal sigma weight residual 93.00 29.39 63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS F 156 " pdb=" SG CYS F 156 " pdb=" SG CYS F 216 " pdb=" CB CYS F 216 " ideal model delta sinusoidal sigma weight residual -86.00 -149.21 63.21 1 1.00e+01 1.00e-02 5.27e+01 ... (remaining 13326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3133 0.075 - 0.150: 294 0.150 - 0.224: 5 0.224 - 0.299: 1 0.299 - 0.374: 1 Chirality restraints: 3434 Sorted by residual: chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CB VAL C 118 " pdb=" CA VAL C 118 " pdb=" CG1 VAL C 118 " pdb=" CG2 VAL C 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 685 " pdb=" N ILE B 685 " pdb=" C ILE B 685 " pdb=" CB ILE B 685 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 3431 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 81 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO B 82 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1339 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A1340 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1340 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1340 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 120 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B 121 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.028 5.00e-02 4.00e+02 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1987 2.74 - 3.28: 22494 3.28 - 3.82: 36565 3.82 - 4.36: 40094 4.36 - 4.90: 69413 Nonbonded interactions: 170553 Sorted by model distance: nonbonded pdb=" OG1 THR C 92 " pdb=" OE1 GLU C 93 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR E 92 " pdb=" OE1 GLU E 93 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLU D 217 " pdb=" OG1 THR D 228 " model vdw 2.202 3.040 nonbonded pdb=" O LEU B 175 " pdb=" OG1 THR B 179 " model vdw 2.224 3.040 nonbonded pdb=" O PRO B1468 " pdb=" OG1 THR B1471 " model vdw 2.230 3.040 ... (remaining 170548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 3 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 126 or resid 147 through 220)) } ncs_group { reference = (chain 'D' and (resid 17 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 143 or resid 154 through 172 or re \ sid 178 through 231)) selection = (chain 'F' and (resid 17 through 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 209 or resid 215 through 231)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.050 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22360 Z= 0.121 Angle : 0.599 11.841 30423 Z= 0.305 Chirality : 0.041 0.374 3434 Planarity : 0.004 0.055 4009 Dihedral : 16.133 89.049 8005 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.67 % Favored : 92.95 % Rotamer: Outliers : 1.55 % Allowed : 21.28 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.16), residues: 2892 helix: 1.69 (0.19), residues: 865 sheet: -0.70 (0.22), residues: 563 loop : -1.51 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.012 0.001 TYR F 70 PHE 0.016 0.001 PHE B 605 TRP 0.012 0.001 TRP B 569 HIS 0.003 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00258 (22352) covalent geometry : angle 0.59886 (30407) SS BOND : bond 0.00158 ( 8) SS BOND : angle 0.54218 ( 16) hydrogen bonds : bond 0.19627 ( 809) hydrogen bonds : angle 6.95791 ( 2259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8588 (tpp) cc_final: 0.8315 (tpp) REVERT: B 685 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6853 (pt) REVERT: A 274 MET cc_start: 0.8892 (tpp) cc_final: 0.8280 (tpt) REVERT: A 572 MET cc_start: 0.7818 (mpp) cc_final: 0.7229 (mpp) REVERT: A 631 MET cc_start: 0.7948 (mmt) cc_final: 0.7307 (mmt) REVERT: A 635 MET cc_start: 0.9424 (mtp) cc_final: 0.9185 (mmm) REVERT: A 990 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7798 (pt) REVERT: A 1322 MET cc_start: 0.5186 (ptt) cc_final: 0.3776 (pmm) REVERT: D 40 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8471 (ttp80) REVERT: F 20 MET cc_start: 0.9518 (pp-130) cc_final: 0.8980 (ppp) REVERT: F 110 MET cc_start: 0.8660 (tpp) cc_final: 0.8301 (tpp) outliers start: 35 outliers final: 28 residues processed: 86 average time/residue: 0.1285 time to fit residues: 18.0049 Evaluate side-chains 80 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 886 SER Chi-restraints excluded: chain B residue 1456 ARG Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1134 ASP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 5.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS A 597 HIS A 628 GLN A 657 GLN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN F 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.044726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.026434 restraints weight = 218750.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.026917 restraints weight = 139710.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.027207 restraints weight = 106614.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.027390 restraints weight = 91377.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.027509 restraints weight = 83469.269| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22360 Z= 0.133 Angle : 0.573 11.250 30423 Z= 0.292 Chirality : 0.041 0.238 3434 Planarity : 0.004 0.053 4009 Dihedral : 5.252 69.850 3245 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.16 % Favored : 92.53 % Rotamer: Outliers : 2.57 % Allowed : 19.12 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2892 helix: 1.69 (0.18), residues: 892 sheet: -0.54 (0.22), residues: 571 loop : -1.56 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1098 TYR 0.013 0.001 TYR F 70 PHE 0.014 0.001 PHE B 605 TRP 0.011 0.001 TRP A 55 HIS 0.004 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00298 (22352) covalent geometry : angle 0.57277 (30407) SS BOND : bond 0.00486 ( 8) SS BOND : angle 0.90026 ( 16) hydrogen bonds : bond 0.03970 ( 809) hydrogen bonds : angle 5.16941 ( 2259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 50 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8066 (ptm) cc_final: 0.7742 (ptm) REVERT: A 274 MET cc_start: 0.8910 (tpp) cc_final: 0.8268 (tpt) REVERT: A 572 MET cc_start: 0.7845 (mpp) cc_final: 0.7306 (mpp) REVERT: A 631 MET cc_start: 0.7746 (mmt) cc_final: 0.7278 (mmt) REVERT: A 990 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7431 (pt) REVERT: A 1322 MET cc_start: 0.5947 (ptt) cc_final: 0.4544 (pmm) REVERT: D 110 MET cc_start: 0.9302 (mmm) cc_final: 0.8618 (tpt) REVERT: F 20 MET cc_start: 0.9367 (pp-130) cc_final: 0.8934 (ppp) REVERT: F 159 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.8874 (t0) outliers start: 58 outliers final: 32 residues processed: 108 average time/residue: 0.1313 time to fit residues: 23.3322 Evaluate side-chains 84 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 221 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 223 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN F 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.044412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.025887 restraints weight = 220773.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026358 restraints weight = 142256.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.026649 restraints weight = 108722.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.026833 restraints weight = 93308.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.026936 restraints weight = 85477.725| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22360 Z= 0.184 Angle : 0.588 11.302 30423 Z= 0.298 Chirality : 0.041 0.232 3434 Planarity : 0.004 0.053 4009 Dihedral : 5.084 69.967 3222 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.75 % Favored : 91.98 % Rotamer: Outliers : 3.36 % Allowed : 19.73 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2892 helix: 1.67 (0.18), residues: 896 sheet: -0.59 (0.22), residues: 550 loop : -1.64 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 623 TYR 0.014 0.001 TYR F 70 PHE 0.017 0.001 PHE A 97 TRP 0.011 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00411 (22352) covalent geometry : angle 0.58781 (30407) SS BOND : bond 0.00469 ( 8) SS BOND : angle 0.93882 ( 16) hydrogen bonds : bond 0.03766 ( 809) hydrogen bonds : angle 4.94560 ( 2259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 50 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8435 (mmt-90) REVERT: B 391 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.8807 (mpp) REVERT: A 111 MET cc_start: 0.8280 (ptm) cc_final: 0.7932 (ptm) REVERT: A 240 MET cc_start: 0.9137 (mmm) cc_final: 0.8826 (mmm) REVERT: A 247 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8605 (pmm) REVERT: A 309 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9176 (p) REVERT: A 572 MET cc_start: 0.7865 (mpp) cc_final: 0.7410 (mpp) REVERT: A 631 MET cc_start: 0.7866 (mmt) cc_final: 0.7304 (mmt) REVERT: A 990 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7393 (pt) REVERT: A 1322 MET cc_start: 0.5925 (ptt) cc_final: 0.4467 (pmm) REVERT: D 110 MET cc_start: 0.9262 (mmm) cc_final: 0.8594 (tpt) REVERT: E 145 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7930 (tm) REVERT: F 20 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8982 (ppp) REVERT: F 71 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8950 (pp) outliers start: 76 outliers final: 43 residues processed: 122 average time/residue: 0.1669 time to fit residues: 32.6983 Evaluate side-chains 99 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 48 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 281 optimal weight: 0.6980 chunk 238 optimal weight: 5.9990 chunk 280 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 82 optimal weight: 0.0170 chunk 47 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN E 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.044427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.025940 restraints weight = 219563.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.026446 restraints weight = 141042.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.026805 restraints weight = 109112.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.026953 restraints weight = 92997.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.027068 restraints weight = 85444.382| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22360 Z= 0.146 Angle : 0.571 11.329 30423 Z= 0.287 Chirality : 0.041 0.152 3434 Planarity : 0.004 0.054 4009 Dihedral : 5.016 72.584 3218 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.37 % Favored : 92.36 % Rotamer: Outliers : 3.54 % Allowed : 19.60 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.16), residues: 2892 helix: 1.69 (0.18), residues: 896 sheet: -0.62 (0.22), residues: 550 loop : -1.63 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.013 0.001 TYR F 70 PHE 0.012 0.001 PHE A 868 TRP 0.011 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00328 (22352) covalent geometry : angle 0.57129 (30407) SS BOND : bond 0.00426 ( 8) SS BOND : angle 0.85890 ( 16) hydrogen bonds : bond 0.03270 ( 809) hydrogen bonds : angle 4.69178 ( 2259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 49 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9634 (OUTLIER) cc_final: 0.8727 (mpp) REVERT: B 672 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: A 111 MET cc_start: 0.8287 (ptm) cc_final: 0.8077 (ptt) REVERT: A 240 MET cc_start: 0.9086 (mmm) cc_final: 0.8723 (mmm) REVERT: A 247 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8598 (pmm) REVERT: A 309 SER cc_start: 0.9536 (OUTLIER) cc_final: 0.9169 (p) REVERT: A 520 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8601 (m170) REVERT: A 572 MET cc_start: 0.7831 (mpp) cc_final: 0.7329 (mpp) REVERT: A 588 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8507 (mmp80) REVERT: A 631 MET cc_start: 0.7786 (mmt) cc_final: 0.7305 (mmt) REVERT: A 990 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6924 (pt) REVERT: A 1322 MET cc_start: 0.6076 (ptt) cc_final: 0.4610 (pmm) REVERT: E 145 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (tm) REVERT: F 20 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8982 (ppp) outliers start: 80 outliers final: 46 residues processed: 123 average time/residue: 0.1239 time to fit residues: 24.9255 Evaluate side-chains 104 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 49 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 190 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.044264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.025745 restraints weight = 219583.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.026205 restraints weight = 141622.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.026517 restraints weight = 111272.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.026691 restraints weight = 95352.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.026803 restraints weight = 86955.216| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22360 Z= 0.174 Angle : 0.584 11.514 30423 Z= 0.294 Chirality : 0.041 0.346 3434 Planarity : 0.004 0.052 4009 Dihedral : 5.029 74.566 3216 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.06 % Favored : 91.67 % Rotamer: Outliers : 3.58 % Allowed : 20.18 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2892 helix: 1.66 (0.18), residues: 895 sheet: -0.76 (0.22), residues: 553 loop : -1.64 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 26 TYR 0.012 0.001 TYR F 70 PHE 0.012 0.001 PHE A 868 TRP 0.015 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00390 (22352) covalent geometry : angle 0.58334 (30407) SS BOND : bond 0.00435 ( 8) SS BOND : angle 0.91395 ( 16) hydrogen bonds : bond 0.03371 ( 809) hydrogen bonds : angle 4.66241 ( 2259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 48 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9623 (OUTLIER) cc_final: 0.8760 (mpp) REVERT: A 240 MET cc_start: 0.9078 (mmm) cc_final: 0.8784 (mmm) REVERT: A 247 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8558 (pmm) REVERT: A 309 SER cc_start: 0.9547 (OUTLIER) cc_final: 0.9183 (p) REVERT: A 520 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8601 (m170) REVERT: A 572 MET cc_start: 0.7789 (mpp) cc_final: 0.7251 (mpp) REVERT: A 588 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8608 (mmp80) REVERT: A 631 MET cc_start: 0.7769 (mmt) cc_final: 0.7249 (mmm) REVERT: A 990 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6972 (pt) REVERT: A 1322 MET cc_start: 0.6316 (ptt) cc_final: 0.4784 (pmm) REVERT: D 40 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8443 (ttp80) REVERT: E 145 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7779 (tm) REVERT: F 20 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8972 (ppp) outliers start: 81 outliers final: 55 residues processed: 124 average time/residue: 0.1201 time to fit residues: 24.3406 Evaluate side-chains 112 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 48 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 145 optimal weight: 0.3980 chunk 215 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1292 ASN ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.044473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026170 restraints weight = 219632.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.026660 restraints weight = 140456.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.026972 restraints weight = 107935.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.027161 restraints weight = 91861.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.027242 restraints weight = 83505.903| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22360 Z= 0.112 Angle : 0.553 13.000 30423 Z= 0.276 Chirality : 0.040 0.231 3434 Planarity : 0.004 0.052 4009 Dihedral : 4.875 76.577 3214 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.74 % Favored : 92.95 % Rotamer: Outliers : 2.92 % Allowed : 21.02 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.16), residues: 2892 helix: 1.74 (0.18), residues: 894 sheet: -0.62 (0.22), residues: 551 loop : -1.63 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.014 0.001 TYR F 70 PHE 0.012 0.001 PHE A 868 TRP 0.025 0.001 TRP A 949 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00257 (22352) covalent geometry : angle 0.55289 (30407) SS BOND : bond 0.00388 ( 8) SS BOND : angle 0.79948 ( 16) hydrogen bonds : bond 0.02896 ( 809) hydrogen bonds : angle 4.44807 ( 2259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 50 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9597 (OUTLIER) cc_final: 0.8769 (mpp) REVERT: A 240 MET cc_start: 0.9075 (mmm) cc_final: 0.8834 (mmm) REVERT: A 247 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8572 (pmm) REVERT: A 274 MET cc_start: 0.8850 (tpp) cc_final: 0.8030 (tpt) REVERT: A 309 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9176 (p) REVERT: A 588 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8610 (mmp80) REVERT: A 631 MET cc_start: 0.7741 (mmt) cc_final: 0.7521 (mmm) REVERT: A 990 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7207 (pt) REVERT: A 1322 MET cc_start: 0.6278 (ptt) cc_final: 0.4743 (pmm) REVERT: D 30 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9196 (p) REVERT: E 145 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7839 (tm) REVERT: F 20 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8997 (ppp) outliers start: 66 outliers final: 48 residues processed: 112 average time/residue: 0.1371 time to fit residues: 24.4915 Evaluate side-chains 104 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 48 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 259 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 240 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 GLN ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.044505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.026245 restraints weight = 218743.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.026724 restraints weight = 139202.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.027114 restraints weight = 104476.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.027231 restraints weight = 89387.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.027311 restraints weight = 83292.616| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22360 Z= 0.115 Angle : 0.557 11.764 30423 Z= 0.276 Chirality : 0.040 0.261 3434 Planarity : 0.004 0.048 4009 Dihedral : 4.827 77.686 3213 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.33 % Favored : 92.32 % Rotamer: Outliers : 3.14 % Allowed : 21.02 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2892 helix: 1.76 (0.18), residues: 894 sheet: -0.60 (0.22), residues: 557 loop : -1.60 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 117 TYR 0.013 0.001 TYR F 70 PHE 0.013 0.001 PHE A 97 TRP 0.013 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00264 (22352) covalent geometry : angle 0.55695 (30407) SS BOND : bond 0.00402 ( 8) SS BOND : angle 0.79516 ( 16) hydrogen bonds : bond 0.02834 ( 809) hydrogen bonds : angle 4.40280 ( 2259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 49 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.8762 (mpp) REVERT: A 240 MET cc_start: 0.9085 (mmm) cc_final: 0.8766 (mmm) REVERT: A 247 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8579 (pmm) REVERT: A 309 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9177 (p) REVERT: A 588 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8574 (mmp80) REVERT: A 631 MET cc_start: 0.7750 (mmt) cc_final: 0.7066 (mmt) REVERT: A 990 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6997 (pt) REVERT: A 1322 MET cc_start: 0.6419 (ptt) cc_final: 0.4943 (pmm) REVERT: D 30 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9192 (p) REVERT: D 40 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8381 (ttp80) REVERT: E 145 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7850 (tm) REVERT: F 20 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9018 (ppp) outliers start: 71 outliers final: 52 residues processed: 117 average time/residue: 0.1374 time to fit residues: 25.2823 Evaluate side-chains 110 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 49 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 87 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 267 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.044536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026322 restraints weight = 218485.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.026800 restraints weight = 140026.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.027063 restraints weight = 105987.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.027262 restraints weight = 91679.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.027357 restraints weight = 83284.419| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22360 Z= 0.110 Angle : 0.557 11.774 30423 Z= 0.274 Chirality : 0.040 0.237 3434 Planarity : 0.004 0.049 4009 Dihedral : 4.793 78.741 3212 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.81 % Favored : 92.84 % Rotamer: Outliers : 2.96 % Allowed : 21.15 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.16), residues: 2892 helix: 1.82 (0.18), residues: 894 sheet: -0.55 (0.22), residues: 564 loop : -1.57 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.013 0.001 TYR F 70 PHE 0.014 0.001 PHE B 600 TRP 0.012 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00255 (22352) covalent geometry : angle 0.55704 (30407) SS BOND : bond 0.00340 ( 8) SS BOND : angle 0.69715 ( 16) hydrogen bonds : bond 0.02710 ( 809) hydrogen bonds : angle 4.32371 ( 2259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 50 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9578 (OUTLIER) cc_final: 0.8756 (mpp) REVERT: A 247 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8580 (pmm) REVERT: A 309 SER cc_start: 0.9530 (OUTLIER) cc_final: 0.9158 (p) REVERT: A 588 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (mmp80) REVERT: A 631 MET cc_start: 0.7830 (mmt) cc_final: 0.7365 (mmt) REVERT: A 990 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6901 (pt) REVERT: A 1322 MET cc_start: 0.6231 (ptt) cc_final: 0.4675 (pmm) REVERT: D 30 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9191 (p) REVERT: D 40 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8342 (ttp80) REVERT: E 145 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7817 (tm) REVERT: F 20 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9017 (ppp) REVERT: F 110 MET cc_start: 0.8600 (tpp) cc_final: 0.8390 (tpp) outliers start: 67 outliers final: 52 residues processed: 114 average time/residue: 0.1524 time to fit residues: 27.3138 Evaluate side-chains 110 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 49 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 144 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN E 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.044312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.025875 restraints weight = 220138.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.026388 restraints weight = 141701.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.026684 restraints weight = 108778.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.026863 restraints weight = 92750.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.027001 restraints weight = 84199.861| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22360 Z= 0.159 Angle : 0.591 11.949 30423 Z= 0.291 Chirality : 0.040 0.213 3434 Planarity : 0.004 0.050 4009 Dihedral : 4.912 78.964 3212 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.88 % Favored : 91.80 % Rotamer: Outliers : 3.10 % Allowed : 21.06 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.16), residues: 2892 helix: 1.80 (0.18), residues: 894 sheet: -0.67 (0.22), residues: 557 loop : -1.57 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 130 TYR 0.012 0.001 TYR F 70 PHE 0.012 0.001 PHE B 600 TRP 0.009 0.001 TRP A 55 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00360 (22352) covalent geometry : angle 0.59085 (30407) SS BOND : bond 0.00353 ( 8) SS BOND : angle 0.88617 ( 16) hydrogen bonds : bond 0.03085 ( 809) hydrogen bonds : angle 4.41571 ( 2259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 49 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.8745 (mpp) REVERT: B 672 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: A 247 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8594 (pmm) REVERT: A 274 MET cc_start: 0.8961 (tpp) cc_final: 0.8155 (tpt) REVERT: A 309 SER cc_start: 0.9537 (OUTLIER) cc_final: 0.9171 (p) REVERT: A 588 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8594 (mmp80) REVERT: A 631 MET cc_start: 0.7753 (mmt) cc_final: 0.7290 (mmt) REVERT: A 990 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6672 (pt) REVERT: A 1322 MET cc_start: 0.6544 (ptt) cc_final: 0.4982 (pmm) REVERT: D 30 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9180 (p) REVERT: D 40 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8398 (ttp80) REVERT: E 145 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7940 (tm) REVERT: F 20 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9050 (ppp) REVERT: F 110 MET cc_start: 0.8647 (tpp) cc_final: 0.7770 (tmm) outliers start: 70 outliers final: 57 residues processed: 116 average time/residue: 0.1348 time to fit residues: 24.5563 Evaluate side-chains 116 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 49 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 48 optimal weight: 0.9980 chunk 230 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 129 optimal weight: 0.2980 chunk 195 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 645 HIS A 888 HIS ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.044219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.025757 restraints weight = 221324.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.026221 restraints weight = 143278.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.026513 restraints weight = 111835.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.026733 restraints weight = 94846.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.026840 restraints weight = 83940.421| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22360 Z= 0.181 Angle : 0.613 14.278 30423 Z= 0.302 Chirality : 0.041 0.202 3434 Planarity : 0.004 0.050 4009 Dihedral : 5.047 76.783 3212 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.68 % Favored : 92.01 % Rotamer: Outliers : 3.19 % Allowed : 21.02 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 2892 helix: 1.74 (0.18), residues: 896 sheet: -0.73 (0.22), residues: 556 loop : -1.60 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 130 TYR 0.014 0.001 TYR F 70 PHE 0.012 0.001 PHE B 600 TRP 0.010 0.001 TRP A1366 HIS 0.005 0.001 HIS A1334 Details of bonding type rmsd covalent geometry : bond 0.00406 (22352) covalent geometry : angle 0.61263 (30407) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.81869 ( 16) hydrogen bonds : bond 0.03208 ( 809) hydrogen bonds : angle 4.47658 ( 2259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 49 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8515 (mmt-90) REVERT: B 572 MET cc_start: 0.8079 (mtt) cc_final: 0.7768 (mmt) REVERT: B 672 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: A 247 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8509 (pmm) REVERT: A 274 MET cc_start: 0.8921 (tpp) cc_final: 0.8128 (tpt) REVERT: A 309 SER cc_start: 0.9546 (OUTLIER) cc_final: 0.9187 (p) REVERT: A 588 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8611 (mmp80) REVERT: A 631 MET cc_start: 0.7755 (mmt) cc_final: 0.7286 (mmt) REVERT: A 990 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6965 (pt) REVERT: A 1322 MET cc_start: 0.6544 (ptt) cc_final: 0.5007 (pmm) REVERT: D 40 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8416 (ttp80) REVERT: E 145 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7944 (tm) REVERT: F 20 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9046 (ppp) outliers start: 72 outliers final: 57 residues processed: 117 average time/residue: 0.1525 time to fit residues: 27.3742 Evaluate side-chains 115 residues out of total 2265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 49 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1377 ARG Chi-restraints excluded: chain C residue 100 CYS Chi-restraints excluded: chain C residue 110 TRP Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LYS Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 54 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 250 optimal weight: 0.9990 chunk 238 optimal weight: 0.0070 chunk 82 optimal weight: 0.0870 chunk 121 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.044656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.026626 restraints weight = 219069.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.027020 restraints weight = 138304.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.027258 restraints weight = 105350.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027498 restraints weight = 92058.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.027573 restraints weight = 83252.888| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22360 Z= 0.096 Angle : 0.561 12.084 30423 Z= 0.277 Chirality : 0.040 0.196 3434 Planarity : 0.004 0.051 4009 Dihedral : 4.769 73.313 3212 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.64 % Favored : 93.02 % Rotamer: Outliers : 2.70 % Allowed : 21.42 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.16), residues: 2892 helix: 1.78 (0.18), residues: 896 sheet: -0.61 (0.22), residues: 556 loop : -1.58 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 396 TYR 0.012 0.001 TYR F 70 PHE 0.013 0.001 PHE B 600 TRP 0.013 0.001 TRP A 55 HIS 0.007 0.001 HIS B 645 Details of bonding type rmsd covalent geometry : bond 0.00222 (22352) covalent geometry : angle 0.56071 (30407) SS BOND : bond 0.00413 ( 8) SS BOND : angle 0.67013 ( 16) hydrogen bonds : bond 0.02486 ( 809) hydrogen bonds : angle 4.21433 ( 2259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.44 seconds wall clock time: 69 minutes 48.58 seconds (4188.58 seconds total)